i'm using Micropython installed on my XBee3 ZigBee module (https://www.sparkfun.com/products/15129).
The Module is plugged into an Arduino Uno Shield and i want to put the output Pins of an analog Heart-Beat-sensor into that shield and read the incoming data from the XBee3 with micropython.

The xbee itself doesn't know anything about what you connect the xbee pins to, so it won't know anything about your arduino shield. But it should be possible to figure out how the funduino board is connected -- i.e. see which arduino pin each xbee pin physically connects to (either by looking at the traces on the board, or using a multimeter in beep-connectivity mode).

That said, this may not actually be possible with the fundunio board you have (unfortunately I don't seem to be able to find anything about it). Historically (before micropython), the way you communicated with an xbee was over the UART and their AT commands (or the more complicated but more flexible API mode, also on the UART). So it's possible that the funduino board only connects the TX/RX pins to the Arduino pins and everything else on the shield is just pass-through from the arduino below to any shield that you connect above it. I think this is very likely.

But -- there appears to be an unpoulated row of pins directly either side of where the xbee sits -- i bet these are connected to the xbee pins. So wire up to them instead of the arduino pins. Or if you actually plan to connect this to an Arduino, then just use a jumper wire to connect them to the arduino pins.

And then of course you can just use machine.Pin.board.Px (look up the datasheet to see which pin is which) on the xbee module.

This has nothing to do with your question but gee I wish the XBee 3 modules had existed when I was last doing Zigbee stuff... (I used the S2B and S2C modules)

What are you using the modules for BTW -- if it's home automation stuff (i.e. Philips Hue / other zigbee lighting etc) then I can send you a bunch of useful stuff.